Methods in Ecology and Evolution

Article	Citations
Cover Picture and Issue Information	766
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Cover Picture and Issue Information	213
Cover Picture and Issue Information	160
Assimilating ecological theory with empiricism: Using constrained generalized additive models to enhance survival analyses	143
Exploring congruent diversification histories with flexibility and parsimony	133
Filtering heart rates using data densities: The boxfilter R package	113
Revticulate: An R framework for interaction with RevBayes	107
AF‐vapeR: A multivariate genome scan for detecting parallel evolution using allele frequency change vectors	96
How to get the most out of phylogenetic imputation without abusing it	95
Using cloud radar to investigate the effect of rainfall on migratory insect flight	86
FlywayNet: A hidden semi‐Markov model for inferring the structure of migratory bird networks from count data	84
OCCUR Shiny application: A user‐friendly guide for curating species occurrence records	84
Not just for programmers: How GitHub can accelerate collaborative and reproducible research in ecology and evolution	80
Beneath the buzz: Quantifying nest locations and densities of ground‐nesting wild bees (Hymenoptera: Anthophila)	78
ECOGEN: Bird sounds generation using deep learning	76
Integrated community occupancy models: A framework to assess occurrence and biodiversity dynamics using multiple data sources	75
A new centrality index designed for multilayer networks	74
Exploring noise, degeneracy and determinism in biological networks with the einet package	73
A network theoretic method for the basic reproductive number for infectious diseases	72
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From anarchy to clarity, data pre‐processing and statistical choices influence quantitative environmental DNA (eDNA) analyses	67
Individual tree extraction through 3D promptable segmentation networks	65

Toward a unified approach to modelling adaptation among demographers and evolutionary ecologists	64
occupancyTuts: Occupancy modelling tutorials with RPresence	61
poems: R package for simulating species' range dynamics using pattern‐oriented validation	60
Nearest neighbour distance matching Leave‐One‐Out Cross‐Validation for map validation	58
plantR: An R package and workflow for managing species records from biological collections	58
Empirical dynamic programming for model‐free ecosystem‐based management	57
Incidence‐data‐based species richness estimation via a Beta‐Binomial model	57
BATScan: A radar classification tool reveals large‐scale bat migration patterns	56
Nighthawk: Acoustic monitoring of nocturnal bird migration in the Americas	55
Cover Picture and Issue Information	52
Long‐term automated visual monitoring of Antarctic benthic fauna	51
EcoEnsemble: A general framework for combining ecosystem models in R	51
Towards biologically realistic estimates of home range and spatial exposure for colonial animals	51
A systematic method for hypothesis synthesis and conceptual model development	51
Continuous on‐board behaviour classification using accelerometry: A case study with a new GPS‐3G‐Bluetooth system in Pacific black ducks	50
Benchmarking imputation methods for categorical biological data	46
Going beyond richness: Modelling the BEF relationship using species identity, evenness, richness and species interactions via the DImodels R package	45
lacunr: Efficient 3D lacunarity for voxelized LiDAR data from forested ecosystems	43
A 3D modelling approach to measuring structural characteristics of bird nest interiors	43
Classifying the activity states of small vertebrates using automated VHF telemetry	42
Scalable semantic 3D mapping of coral reefs with deep learning	42
MoonShine: A software‐hardware system for simulating moonlight ground illuminance and re‐creating artificial moonlight cycles in a laboratory environment	41
Dynamic visualisation of million‐tip trees: The OneZoom project	40
Multi‐trait point pattern reconstruction of plant ecosystems	37
An open future for MEE	37
Gone with the wind: Inferring bird migration with light‐level geolocation, wind and activity measurements	37
treetop: A Shiny‐based application and R package for extracting forest information from LiDAR data for ecologists and conservationists	37
Navigating through space and time: A methodological approach to quantify spatiotemporal connectivity using stream flow data as a case study	36
A general framework for jointly modelling thermal and hydric constraints on developing eggs	36
The ecological forecast limit revisited: Potential, absolute and relative system predictability	36
Chronospaces: An R package for the statistical exploration of divergence times promotes the assessment of methodological sensitivity	33
Cover Picture and Issue Information	32
Integrated movement models for individual tracking and species distribution data	32
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Corrigendum	32
Plant biodiversity assessment through soil eDNA reflects temporal and local diversity	32
qad: An R‐package to detect asymmetric and directed dependence in bivariate samples	31
PleistoDist: A toolbox for visualising and quantifying the effects of Pleistocene sea‐level change on island archipelagos	31
A Double machine learning trend model for citizen science data	31
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Using causal diagrams and superpopulation models to correct geographic biases in biodiversity monitoring data	31
Sourcing high tissue quality brains from deceased wild primates with known socio‐ecology	30
An aquaria set‐up for long‐term, multiple‐stressor research in marine organisms	30
The Wayqecha Amazon Cloud Curtain Ecosystem Experiment: A new experimental method to manipulate fog water inputs in terrestrial systems	29
Retrodiction of forest demography: Backward simulation with reverse matrix models	29
treats: A modular R package for simulating trees and traits	29
Using standardized fish‐specific autonomous reef monitoring structures (FARMS) to quantify cryptobenthic fish communities	29
When to monitor or control: Informed invasive species management using a partially observable Markov decision process (POMDP) framework	29
Linear polyacrylamide is highly efficient in precipitating and purifying environmental and ancient DNA	29
TinyCO2: High‐performance, low‐cost CO2 enrichment for field‐grown plants	28

RFIDeep: Unfolding the potential of deep learning for radio‐frequency identification	28
Introducing recurrent event analyses to assess species interactions based on camera‐trap data: A comparison with time‐to‐first‐event approaches	28
The r package enerscape: A general energy landscape framework for terrestrial movement ecology	28
PicoCam: High‐resolution 3D imaging of live animals and preserved specimens	28
Measuring understorey vegetation structure using a novel mixed‐reality device	28
Issues in calibrating models with multiple unbalanced constraints: the significance of systematic model and data errors	28
Cover Picture and Issue Information	27
Existing and emerging uses of drones in restoration ecology	27
Parasitic flowering plant collections embody the extended specimen	26
Accelerating advances in landscape connectivity modelling with the ConScape library	26
Same data, different results? Machine learning approaches in bioacoustics	26
Integrated SDM database: Enhancing the relevance and utility of species distribution models in conservation management	26
Overall dynamic body acceleration measures activity differently on large versus small aquatic animals	26
The Benthic Underwater Microscope imaging PAM (BUMP): A non‐invasive tool for in situ assessment of microstructure and photosynthetic efficiency	26
Reflectance spectroscopy allows rapid, accurate and non‐destructive estimates of functional traits from pressed leaves	25
Handbook of protocols for standardized measurements of floral traits for pollinators in temperate communities	25
RevGadgets: An R package for visualizing Bayesian phylogenetic analyses from RevBayes	25
Food web reconstruction through phylogenetic transfer of low‐rank network representation	25
Automated identification of diverse Neotropical pollen samples using convolutional neural networks	25
Detecting and reducing heterogeneity of error in acoustic classification	25
Methods for testing publication bias in ecological and evolutionary meta‐analyses	24
Optimising sampling designs for habitat fragmentation studies	24
Hidden Markov models: Pitfalls and opportunities in ecology	24
Generating spatially realistic environmental null models with the shift‐&‐rotate approach helps evaluate false positives in species distribution modelling	24
Use of amino acid isotope analysis to investigate capital versus income breeding strategies in migratory avian species	23
Detecting seasonal episodic‐like spatio‐temporal memory patterns using animal movement modelling	23
TreeCompR: Tree competition indices for inventory data and 3D point clouds	23
A wireless, remotely operable and easily customizable robotic flower system	23
In situ estimation of active dispersal abilities in reef fish early life stages using tracking technologies	23
A process approach to quality management doublesNEONsensor data quality	22
Limits to ecological forecasting: Estimating uncertainty for critical transitions with deep learning	22
Correction to: Quantifying degradation in animal acoustic signals with the R package baRulho	21
Estimating process‐based model parameters from species distribution data using the evolutionary algorithm CMA‐ES	21
Writing a massively multi‐authored paper: Overcoming barriers to meaningful authorship for all	21
Tracking the frequency of phytoplankton clonal lineages using multispectral image flow cytometry and neural networks	21
An automatic classifier of bat sonotypes around the world	21
Addressing spatial confounding in geostatistical regression models: An R‐INLA approach	21
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OpenSoundscape: An open‐source bioacoustics analysis package for Python	20
The power of forecasts to advance ecological theory	20
Cover Picture and Issue Information	20
TaxoNERD: Deep neural models for the recognition of taxonomic entities in the ecological and evolutionary literature	20
A cost‐effective method to passively sample communities at the forest canopy–aerosphere interface	20
The Movebank system for studying global animal movement and demography	20
The CV is dead, long live the CV!	20
tidysdm: Leveraging the flexibility of tidymodels for species distribution modelling in R	19
Using ensemble methods to improve the robustness of deep learning for image classification in marine environments	19
starve: An R package for spatio‐temporal analysis of research survey data using nearest‐neighbour Gaussian processes	19
sabinaNSDM: An R package for spatially nested hierarchical species distribution modelling	19
NAPS: Integrating pose estimation and tag‐based tracking	19
Impact of sampling strategy on inference of community assembly processes in phylogenetic island biogeography	18
Design and performance of an ecosystem‐scale forest soil warming experiment with infrared heater arrays	18
Scalable phylogenetic Gaussian process models improve the detectability of environmental signals on local extinctions for many Red List species	18
Monitoring fast‐moving animals—Building a customized camera system and evaluation toolset	18
soundClass: An automatic sound classification tool for biodiversity monitoring using machine learning	18
Methods to account for incomplete viewsheds in distance sampling	18
poolHelper: An R package to help in designing Pool‐Seq studies	18
Synthesizing forecasts to inform decision‐making and advance ecological theory	18
Towards scalable insect monitoring: Ultra‐lightweight CNNs as on‐device triggers for insect camera traps	18
DeepDiveR—A software for deep learning estimation of palaeodiversity from fossil occurrences	18
The uniform AUC: Dealing with the representativeness effect in presence–absence models	18
Estimating interaction strengths for diverse horizontal systems using performance data	18
Guidelines for the prediction of species interactions through binary classification	18
PhycoCanopy: An R Shiny tool for exploring primary production in macroalgal canopies	17
ipsecr: An R package for awkward spatial capture–recapture data	17
A framework to model a web of linkage disequilibria for natural allotetraploid populations	17
Managing risk and uncertainty in systematic conservation planning with insufficient information	17
Cover Picture and Issue Information	17
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Estimating species misclassification with occupancy dynamics and encounter rates: A semi‐supervised, individual‐level approach	17
Precise tactile stimulation of worker ants by a robotic manipulator reveals that individual responses are density‐ and context‐dependent	17
Unifying individual differences in personality, predictability and plasticity: A practical guide	17
soundscape_IR: A source separation toolbox for exploring acoustic diversity in soundscapes	17
Cover Picture and Issue Information	17
Temporal design for aquatic organismal sampling across the National Ecological Observatory Network	17
Evo‐Scope: Fully automated assessment of correlated evolution on phylogenetic trees	17
The Latent Dirichlet Allocation model applied to airborne LiDAR data: A case study on mapping forest degradation associated with fragmentation and fire in the Amazon region	17
Practical guidelines and the EMLN R package for handling ecological multilayer networks	17
How to generate accurate continuous thermal regimes from sparse but regular temperature measurements	17
aniMotum, an R package for animal movement data: Rapid quality control, behavioural estimation and simulation	17

Cover Picture and Issue Information	17
A framework for post‐processing bird tracks from automated tracking radar systems	16
Including the invisible fraction in whole population studies: A guide to the genetic sampling of unhatched bird eggs	16
Stable isotope fingerprinting traces essential amino acid assimilation and multichannel feeding in a vertebrate consumer	16
Improved order selection method for hidden Markov models: A case study with movement data	16
Quantifying the utilisation of blue, green and brown resources by riparian predators: A combined use of amino acid isotopes and fatty acids	16
A GLMM approach for combining multiple relative abundance surfaces	16
Introducing the combined atlas framework for large‐scale web‐based data visualization: The GloNAF atlas of plant invasion	16
Correction to ‘The Aquatic Metatron: A large‐scale experimental facility to study the combined effects of habitat fragmentation and climate change on aquatic meta‐ecosystems’	16
A conceptual framework for host‐associated microbiomes of hybrid organisms	16
Acoustic and archival technologies join forces: A combination tag	16
Sources of uncertainty in DNA metabarcoding of whole communities: Implications for its use in biomonitoring	16
Pitfalls arising from site selection bias in population monitoring defy simple heuristics	16
PiCAM: A Raspberry Pi‐based open‐source, low‐power camera system for monitoring plant phenology in Arctic environments	16
The use of weighted averages of Hedges' d in meta‐analysis: Is it worth it?	16
Long‐term collar deployment leads to bias in soil respiration measurements	16
CaptuRING: A do‐it‐yourself tool for wood sample digitization	16
Hard tissue thin‐sectioning techniques in vertebrate paleohistology: Review, synthesis and improvements	16
Population assignment from genotype likelihoods for low‐coverage whole‐genome sequencing data	16
allodb: An R package for biomass estimation at globally distributed extratropical forest plots	15
Studying collective animal behaviour with drones and computer vision	15
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Cover Picture and Issue Information	15
ecochange: An R‐package to derive ecosystem change indicators from freely available earth observation products	15
Extending isolation by resistance to predict genetic connectivity	15
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Real‐time alerts from AI‐enabled camera traps using the Iridium satellite network: A case‐study in Gabon, Central Africa	15
A low‐cost IoT network to monitor microclimate variables in ecosystems	15
Streamlining analysis methods for large acoustic surveys using automatic detectors with operator validation	15
bistro: An R package for vector bloodmeal identification by short tandem repeat overlap	15
HSC3D: A Python package to quantify three‐dimensional habitat structural complexity	14
TransMCL enables the assembly of full‐length coding genes for collecting complete hierarchical orthogroups	14
Analysing biodiversity observation data collected in continuous time: Should we use discrete‐ or continuous‐time occupancy models?	14
Estimating animal density for a community of species using information obtained only from camera‐traps	14
3D photogrammetry and deep‐learning deliver accurate estimates of epibenthic biomass	14
Realising the promise of large data and complex models	14
rphenoscate: An R package for semantics‐aware evolutionary analyses of anatomical traits	14
A continuous‐score occupancy model that incorporates uncertain machine learning output from autonomous biodiversity surveys	14
Sap Flow Analyzer: A tool to standardize sap flow estimation and scaling to whole‐tree water use using the HFD method	14
ISSRseq: An extensible method for reduced representation sequencing	14
Cover Picture and Issue Information	14
PoolDilutionR: An R package for easy optimization of isotope pool dilution calculations	14
isotracer: An R package for the analysis of tracer addition experiments	14
CATS: A high‐performance software framework for simulating plant migration in changing environments	14
ENphylo: A new method to model the distribution of extremely rare species	13
HemiPy: A Python module for automated estimation of forest biophysical variables and uncertainties from digital hemispherical photographs	13
Cost‐effective seafloor habitat mapping using a portable speedy sea scanner and deep‐learning‐based segmentation: A sea trial at Pujada Bay, Philippines	13
Corrigendum	13
Estimating forest above‐ground biomass with terrestrial laser scanning: Current status and future directions	13
Continuous‐surface geographic assignment of migratory animals using strontium isotopes: A case study with monarch butterflies	13
Investigating soil mesofauna cryptic diversity: Current challenges and perspectives	13
The role of large language models in interdisciplinary research: Opportunities, challenges and ways forward	13
Impact of acoustic index parameters on soundscape comparisons	13
Generating continuous maps of genetic diversity using moving windows	13
Cover Picture and Issue Information	13
Cover Picture and Issue Information	13
rphylopic: An R package for fetching, transforming, and visualising PhyloPic silhouettes	13
ChirpArray: A low‐cost, easy‐to‐construct microphone array for long‐term ecoacoustic monitoring	13
Correction to ‘PhyBaSE: A Bayesian structural equation model approach to causal inference in phylogenetic comparative analyses’	13
Regional ecological forecasting across scales: A manifesto for a biodiversity hotspot	13
Applying computer vision to digitised natural history collections for climate change research: Temperature‐size responses in British butterflies	13
Connectivity conservation planning through deep reinforcement learning	13
Ten practical guidelines for microclimate research in terrestrial ecosystems	13
Clustering and unconstrained ordination with Dirichlet process mixture models	13
A model selection approach to structural equation modelling: A critical evaluation and a road map for ecologists	13
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An RGB‐D framework for capturing soft‐sediment microtopography	12
mpmsim: An R package for simulating matrix population models	12
A new tool to improve the estimates of interaction rewiring considering the whole community composition	12
ohun: An R package for diagnosing and optimizing automatic sound event detection	12
A multi‐property assessment of intensity of use provides a functional understanding of animal movement	12
ontophylo: Reconstructing the evolutionary dynamics of phenomes using new ontology‐informed phylogenetic methods	12
High‐magnification platform for characterising microscopic communities	12
AMMonitor 2: Remote monitoring of biodiversity in an adaptive framework in R	12
Reconstructing bird trajectories from pressure and wind data using a highly optimized hidden Markov model	12
plantTracker: An R package to translate maps of plant occurrence into demographic data	12
Simple assay quantifying sediment resuspension effects on marine carbon storage	12
Decoding the footsteps of the African savanna: Classifying wildlife using seismic signals and machine learning	12
EEMtoolbox: A user‐friendly R package for flexible ensemble ecosystem modelling	12
Wellcounter: Automated high‐throughput phenotyping for aquatic microinvertebrates	12
Avoiding confusion: Modelling image identification surveys with classification errors	12
Bioregionalization analyses with the bioregion R package	12
Distinguishing passive and driven trait evolution in the presence of boundaries	11
Systematic review and best practices for drone remote sensing of invasive plants	11
Cover Picture and Issue Information	11
Mitigating pseudoreplication and bias in resource selection functions with autocorrelation‐informed weighting	11
Robust passive sampling of airborne environmental DNA to monitor plants and animals	11
patter: Particle algorithms for animal tracking in R and Julia	11
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Navigating the temporal continuum of effective population size	11
Deep reinforcement learning for conservation decisions	11
A heuristic method to evaluate consequences for flight control and stability induced by attachment of biologging devices to birds and bats	11
A Monte Carlo resampling framework for implementing goodness‐of‐fit tests in spatial capture‐recapture models	11
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metaRange: A framework to build mechanistic range models	11